Others have suggested some great tools but they all generally require installation, setup, and some non-trivial learning curve. By all means dive in and try those apps, but if all you want to do is punch a rectangular hole in the STL those options might not be the simplest way to get the job done.
For simple tasks like this (and for some lightweight design work) I use a free online tool called TinkerCAD. It’s a web-based CAD environment, so you just open the site in your browser and start working. You can import STL files easily, modify them, then export as a new STL file. I do this a lot for customers who upload partially broken designs that might not meet their requirements. It’s also a handy way to chop up an STL file that would best be printed as two halves.
